Background: Evidence-based complementary treatment options for multiple sclerosis (MS) are limited. Objective: To investigate the effect of hippotherapy plus standard care versus standard care alone in MS patients. Methods: A total of 70 adults with MS were recruited in five German centers and randomly allocated to the intervention group (12 weeks of hippotherapy) or the control group. Primary outcome was the change in the Berg Balance Scale (BBS) after 12 weeks, and further outcome measures included fatigue, pain, quality of life, and spasticity. Results: Covariance analysis of the primary endpoint resulted in a mean difference in BBS change of 2.33 (95% confidence interval (CI): 0.03–4.63, p = 0.047) between intervention (n = 32) and control (n = 38) groups. Benefit on BBS was largest for the subgroup with an Expanded Disability Status Scale (EDSS) ⩾ 5 (5.1, p = 0.001). Fatigue (−6.8, p = 0.02) and spasticity (−0.9, p = 0.03) improved in the intervention group. The mean difference in change between groups was 12.0 (p < 0.001) in physical health score and 14.4 (p < 0.001) in mental health score of Multiple Sclerosis Quality of Life-54 (MSQoL-54). Conclusion: Hippotherapy plus standard care, while below the threshold of a minimal clinically important difference, significantly improved balance and also fatigue, spasticity, and quality of life in MS patients.